Genetic approaches to measuring connectivity

Oceanography

Volumn 20, Issue SPL.ISS. 3, 2007, Pages 70-79

  Hedgecock, Dennis ^a   Barber, Paul H ^b   Edmands, Suzanne ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 52649089000     PISSN: 10428275     EISSN: None     Source Type: Journal    
DOI: 10.5670/oceanog.2007.30     Document Type: Article

References (80)

1. Abdo, Z., K.A. Crandall, and P. Joyce. 2004. Evaluating the performance of likelihood methods for detecting population structure and migration. Molecular Ecology 13:837-851.
2. Allendorf, F.W. 1986. Genetic drift and the loss of alleles versus heterozygosity. Zoo Biology 5:181-190.
3. Árnason, E. 2004. Mitochondrial cytochrome b DNA variation in the high-fecundity Atlantic cod: Trans-Atlantic clines and shallow gene genealogy. Genetics 166:1,871-1,885.
4. Barber, P.H., S.R. Palumbi, M.V. Erdmann, and M.K. Moosa. 2000. A marine Wallace's line? Nature 406:692-693.
5. Barber, P.H., S.R. Palumbi, M.V. Erdmann and M.K. Moosa. 2002. Sharp genetic breaks among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to larval transport: Patterns, causes, and consequences. Molecular Ecology 11:659-674.
6. Baums, I.B., M.W. Miller, and M.E. Hellberg. 2005. Regionally isolated populations of an imperiled Caribbean coral, Acropora palmate. Molecular Ecology 14:1,377-1,390.
7. Beckenbach, A.T. 1994. Mitochondrial haplotype frequencies in oyster: Neutral alternatives to selection models. Pp. 188-198 in Non-Neutral Evolution Theories and Molecular Data. B. Golding, ed., Chapman and Hall, NY.
8. Beerli, P., and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences of the United States of America 98:4,563-4,568.
9. Benzie, J.A.H. 1999. Genetic structure of coral reef organisms: Ghosts of dispersal past. American Zoologist 39:131-145.
10. Benzie, J.A.H., and S.T. Williams. 1997. Genetic structure of giant clam (Tridacna maxima) populations in the west Pacific is not consistent with dispersal by present-day ocean currents. Evolution 51:768-783.
11. Bernardi, G., and A. Vagelli. 2004. Population structure in Banggai cardinalfish, Pterapogon kauderni, a coral reef species lacking a pelagic larval phase. Marine Biology 145:803-810.
12. Bierne, N., S. Launey, Y. Naciri-Graven, and F. Bonhomme. 1998. Early effect of inbreeding as revealed by microsatellite analyses on Ostrea edulis larvae. Genetics 148:1,893-1,906.
13. Block, B.A., H. Dewar, C. Farwell, and E.D. Prince. 1998. A new satellite technology for tracking the movements of Atlantic bluefin tuna. Proceedings of the National Academy of Sciences of the United States of America. 95:9,384-9,389.
14. Buroker, N.E. 1983. Population genetics of the American oyster Crassostrea virginica along the Atlantic coast and the Gulf of Mexico. Marine Biology 75:99-112.
15. Burton, R.S. 1997. Genetic evidence for long term persistence of marine invertebrate populations in an ephemeral environment. Evolution 51:993-998.
16. Burton, R.S., and M.W. Feldman. 1981. Population genetics of Tigriopus californicus: II. Differentiation among neighboring populations. Evolution 35:1,192-1,205.
17. Burton, R.S., and B.-N. Lee. 1994. Nuclear and mitochondrial gene genealogies and allozyme polymorphism across a major phylogeographic break in the copepod Tigriopus californicus. Proceedings of the National Academy of Sciences on the United States of America. 91:5,197-5,201.
18. Cornuet, J.M., S. Piry, G. Luikart, A. Estoup, and M. Solignac. 1999. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153:1,989-2,000.
19. Cowen, R.K., C.B. Paris, and A. Srinivasan. 2006. Scaling of connectivity in marine populations. Science 311:522-527.
20. Edmands, S. 2001. Phylogeography of the intertidal copepod Tigriopus californicus reveals substantially reduced population differentiation at northern latitudes. Molecular Ecology 10:1,743-1,750.
21. Edmands, S., and J.S. Harrison. 2003. Molecular and quantitative trait variation within and among populations of the intertidal copepod Tigriopus californicus. Evolution 57:2,277-2,285.
22. Edmands, S., P.E. Moberg, and R.S. Burton. 1996. Allozyme and mitochondrial DNA evidence of population subdivision in the purple sea urchin Strongylocentrotus purpuratus. Marine Biology 126:443-450.
23. Flowers, J.M., S.C. Schroeter, and R.S. Burton. 2002. The recruitment sweepstakes has many winners: Genetic evidence from the sea urchin Strongylocentrotus purpuratus. Evolution 56:1445-1453.
24. Frankham, R. 1995. Effective population-size adultpopulation size ratios in wildlife: A review. Genetical Research 66:95-107.
25. Galindo, H.M., D.B. Olson, and S.R. Palumbi. 2006. Seascape genetics: A coupled oceanographicgenetic model predicts population structure of Caribbean corals. Current Biology 16:1,622-1,626.
26. Glynn, P.W. 1988. El Nino-Southern Oscillation 1982-1983: Nearshore population, community, and ecosystem responses. Annual Review of Ecology and Systematics 19:309-345.
27. Hardy, O.J., and X. Vekemans. 1999. Isolation by distance in a continuous population: Reconciliation between spatial autocorrelation analysis and population genetics models. Heredity 83:145-154.
28. Hare, M.P., S.K. Allen Jr., P. Bloomer, M.D. Camara, R.B. Carnegie, J. Murfree, M. Luckenbach, D. Meritt, C. Morrison, K. Paynter, and others. 2006. A genetic test for recruitment enhancement in Chesapeake Bay oysters, Crassostrea virginica, after population supplementation with a disease tolerant strain. Conservation Genetics 7:717-734.
29. Hauser, L., G.J. Adcock, P.J. Smith, J.H. Bernal Ramírez, and G.R. Carvalho. 2002. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proceedings of the National Academy of Sciences of the United States of America 99: 11,742-11,1747.
30. Hedgecock, D. 1986. Is gene flow from pelagic larval dispersal important in the adaptation and evolution of marine invertebrates? Bulletin of Marine Science 39:550-564.
31. Hedgecock, D. 1994. Does variance in reproductive success limit effective population size of marine organisms? Pp. 122-134 in Genetics and Evolution of Aquatic Organisms. A. Beaumont, ed., Chapman & Hall, London.
32. Hedgecock, D., and F. Sly. 1990. Genetic drift and effective population sizes of hatchery-propagated stocks of the Pacific oyster, Crassostrea gigas. Aquaculture 88:21-38.
33. Hedgecock, D., S. Launey, A.I. Pudovkin, Y. Naciri, S. Lapègue, and F. Bonhomme. 2007. Small effective number of parents (Nb) inferred for a naturally spawned cohort of juvenile European flat oysters Ostrea edulis. Marine Biology 150:1,173-1,182.
34. Hedrick, P. 2005a. A standardized genetic differentiation measure. Evolution 59:1,633-1,638.
35. Hedrick, P. 2005b. Large variance in reproductive success and the Ne/N ratio. Evolution 59:1,596-1,599.
36. Hellberg, M.E., R.S. Burton, J.E. Neigel, and S.R. Palumbi. 2002. Genetic assessment of connectivity among marine populations. Bulletin of Marine Science 70:273-290.
37. Hoarau, G., E. Boon, D.N. Jongma, S. Ferber, J. Palsson, H.W. Van der Veer, A.D. Rijnsdorp, W.T. Stam, and J.L. Olsen. 2005. Low effective population size and evidence for inbreeding in an overexploited flatfish, plaice (Pleuronectes platessa L.). Proceedings of the Royal Society B-Biological Sciences 272:497-503.
38. Jones, G.P., M.J. Milicich, M.J. Emslie, and C. Lunow. 1999. Self-recruitment in a coral reef fish population. Nature 402:802-804.
39. Jones, G.P., S. Planes, and S.R. Thorrold. 2005. Coral reef fish larvae settle close to home. Current Biology 15:1,314-1,318.
40. Karl, S.A., and J.C. Avise. 1992. Balancing selection at allozyme loci in oysters: Implications from nuclear RFLPs. Science 256:100-102.
41. Koehn, R.K., R.I.E. Newell, and F. Immermann. 1980. Maintenance of an aminopeptidase allele frequency cline by natural-selection. Proceedings of the National Academy of Sciences of the United States of America 77:5,385-5,389.
42. Knutsen, H., P.E. Jorde, C. André, and N.C. Stenseth. 2003. Fine-scaled geographical population structuring in a highly mobile marine species: The Atlantic cod. Molecular Ecology 12:385-394.
43. Kobayashi, D.R. 2006. Colonization of the Hawaiian Archipelago via Johnston Atoll: A characterization of oceanographic transport corridors for pelagic larvae using computer simulation. Coral Reefs 25:407-417.
44. Launey, S., and D. Hedgecock 2001. High genetic load explains segregation distortion and heterosis in a bivalve mollusc. Genetics 159:255-265.
45. Li, G., and D. Hedgecock 1998. Genetic heterogeneity detected by PCR-SSCP, among samples of larval Pacific oysters (Crassostrea gigas Thunberg), supports the hypothesis of large variance in reproductive success. Canadian Journal of Fisheries and Aquatic Sciences 55:1,025-1,033.
46. Lobel, P.S. 1997. Comparative settlement age of damselfish larvae (Plectroglyphidodon imparipennis, Pomacentridae) from Hawaii and Johnston Atoll. Biological Bulletin 193:281-283.
47. Luikart, G., and J.M. Cornuet. 1999. Estimating the effective number of breeders from heterozygote excess in progeny. Genetics 151:1,211-1,216.
48. Maes, G.E., J.M. Pujolar, B. Hellemans, and F.A.M. Volckaert. 2006. Evidence for isolation by time in the European eel (Anguilla anguilla L.). Molecular Ecology 15:2,095-2,107.
49. Manel, S., M.K. Schwartz, G. Luikart, and P. Taberlet. 2003. Landscape genetics: Combining landscape ecology and population genetics. Trends in Ecology and Evolution 18:189-196.
50. Manel, S., O.E. Gaggioti, and R.S. Waples. 2005. Assignment methods: Matching biological questions with appropriate techniques. Trends in Ecology and Evolution 20:136-142.
51. Mayr, E. 1963. Animal Species and Evolution. Harvard, Belknap Press, Cambridge, MA.
52. McDonald, J.H., B.C. Verrelli, and L.B. Geyer. 1996. Lack of geographic variation in anonymous nuclear polymorphisms in the American oyster, Crassostrea virginica. Molecular Biology and Evolution 13:1,114-1,118.
53. Moberg, P.E., and R.S. Burton. 2000. Genetic heterogeneity among adult and recruit red sea urchins, Stronglyocentrotus franciscanus. Marine Biology 136:773-784.
54. Nielsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation: A Markov Chain Monte Carlo approach. Genetics 158:885-896.
55. Nunney, L. 1996. The influence of variation in female fecundity on effective population size. Biological Journal of the Linnean Society 59:411-425.
56. Paetkau, D., W. Calvert, I. Stirling, and C. Strobeck. 1995. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 4:347-354.
57. Palumbi, S.R. 2003. Population genetics, demographic connectivity, and the design of marine reserves. Ecological Applications 13:S146-S158.
58. Planes, S., and P.J. Doherty. 1997. Genetic and color interaction at a contact zone of Acanthochromis polyacanthus: A marine fish lacking pelagic larvae. Evolution 51:1,232-1,243.
59. Planes, S., and P. Lenfant. 2002. Temporal change in the genetic structure between and within cohorts of a marine fish, Diplodus sargus, induced by a large variance in individual reproductive success. Molecular Ecology 11:1,515-1,524.
60. Pudovkin, A.I., D.V. Zaykin, and D. Hedgecock. 1996. On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics 144:383-387.
61. Pujolar, J.M., G.E. Maes, and F.A.M. Volckaert. 2006. Genetic patchiness among recruits in the European eel Anguilla anguilla. Marine Ecology-Progress Series 307:209-217.
62. Reeb, C.A., and J.C. Avise. 1990. A genetic discontinuity in a continuously distributed species: Mitochondrial DNA in the American oyster, Crassostrea virginica. Genetics 124:397-406.
63. Selkoe, K.A., S.D. Gaines, J. E. Caselle, and R.R. Warner. 2006. Current shifts and kin aggregation explain genetic patchiness in fish recruits. Ecology 87:3,082-3,094.
64. Slatkin, M. 1993. Isolation by distance in equilibrium and nonequilibrium populations. Evolution 47:264-279.
65. Slatkin, M. 2005. Seeing ghosts: The effect of unsampled populations on migration rates estimated for sampled populations. Molecular Ecology 14:67-73.
66. Song, S., D.K. Dey, and K.E. Holsinger. 2006. Differentiation among populations with migration, mutation, and drift: Implications for genetic inference. Evolution 60:1-12.
67. Sotka, E.E., and S.R. Palumbi. 2006. The use of genetic clines to estimate dispersal distances of marine larvae. Ecology 87:1,094-1,103.
68. Sotka, E.E., J. P Wares, J.B. Barth, R.K. Grosberg, and S.R. Palumbi. 2004. Strong genetic clines and geographic variation in gene flow in the rocky intertidal barnacle Balanus glandula. Molecular Ecology 13:2,143-2,156.
69. Stenseth, N.C., P.E. Jorde, K.S. Chan, E. Hansen, H. Knutsen, C. Andre, M.D. Skogen, K. Lekve. 2006. Ecological and genetic impact of Atlantic cod larval drift in the Skagerrak. Proceedings of the Royal Society B-Biological Sciences 273:1,085-1,092.
70. Swearer, S.E., J.E. Caselle, D.W. Lea, and R.R. Warner. 1999. Larval retention and recruitment in an island population of a coral-reef fish. Nature 402:799-802.
71. Thorrold, S.R., C. Latkoczy, P.K. Swart, C.M. Jones. 2001. Natal homing in a marine fish metapopulation. Science 291:297-299.
72. Treml, E.A. 2006. Modeling marine larval dispersal: A graph-theoretic approach for evaluating coral reef connectivity. Ph.D. Dissertation, Duke University, Durham, NC.
73. Turner, T.F., J.P. Wares, and J.R. Gold. 2002. Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, estuarine-dependent marine fish (Sciaenops ocellatus). Genetics 162:1,329-1,339.
74. Underwood, J.N., L.D. Smith, M.J. Van Oppen, and J.P. Gilmour. 2007. Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching. Molecular Ecology 16:1,771-1,784.
75. Waples, R.S. 1998. Separating the wheat from the chaff: Patterns of genetic differentiation in high gene flow species. Journal of Heredity 89:438-450.
76. Waples, R.S. 2002. Evaluating the effect of stage-specific survivorship on the Ne/N ratio. Molecular Ecology 11:1,029-1,037.
77. Waples, R.S., and O. Gaggiotti. 2006. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15:1,419-1,439.
78. Whitlock, M.C., and D.E. McCauley. 1999. Indirect measures of gene flow and migration: FST ≠ 1/(4Nm+1). Heredity 82:117-125.
79. Wilson, G.A., and B. Rannala. 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163:1,177-1,191.
80. Wright, S. 1931. Evolution in Mendelian populations. Genetics 28:139-156.